Starting phenix.real_space_refine on Thu Jul 2 17:24:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8tzr_41767/07_2026/8tzr_41767.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tzr_41767/07_2026/8tzr_41767.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8tzr_41767/07_2026/8tzr_41767.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tzr_41767/07_2026/8tzr_41767.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8tzr_41767/07_2026/8tzr_41767.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tzr_41767/07_2026/8tzr_41767.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8tzr_41767/07_2026/8tzr_41767.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8tzr_41767/07_2026/8tzr_41767.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.060 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 72 5.16 5 C 5668 2.51 5 N 1479 2.21 5 O 1601 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8821 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2453 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 12, 'TRANS': 300} Chain: "B" Number of atoms: 4010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 4010 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 21, 'TRANS': 471} Chain: "C" Number of atoms: 2218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2218 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 11, 'TRANS': 261} Chain breaks: 1 Chain: "D" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'GLC': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "A" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'PAM': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PAM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Time building chain proxies: 1.51, per 1000 atoms: 0.17 Number of scatterers: 8821 At special positions: 0 Unit cell: (97.11, 121.18, 135.29, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 72 16.00 P 1 15.00 O 1601 8.00 N 1479 7.00 C 5668 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 42 " - pdb=" SG CYS A 56 " distance=2.03 Simple disulfide: pdb=" SG CYS A 77 " - pdb=" SG CYS A 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 138 " - pdb=" SG CYS A 155 " distance=2.03 Simple disulfide: pdb=" SG CYS A 203 " - pdb=" SG CYS A 217 " distance=2.03 Simple disulfide: pdb=" SG CYS A 205 " - pdb=" SG CYS A 212 " distance=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 312 " distance=2.03 Simple disulfide: pdb=" SG CYS A 297 " - pdb=" SG CYS A 307 " distance=2.03 Simple disulfide: pdb=" SG CYS A 311 " - pdb=" SG CYS A 351 " distance=2.03 Simple disulfide: pdb=" SG CYS A 327 " - pdb=" SG CYS A 342 " distance=2.03 Simple disulfide: pdb=" SG CYS A 329 " - pdb=" SG CYS A 339 " distance=2.03 Simple disulfide: pdb=" SG CYS A 334 " - pdb=" SG CYS A 335 " distance=2.03 Simple disulfide: pdb=" SG CYS B 50 " - pdb=" SG CYS B 71 " distance=2.02 Simple disulfide: pdb=" SG CYS B 162 " - pdb=" SG CYS B 179 " distance=2.03 Simple disulfide: pdb=" SG CYS C 105 " - pdb=" SG CYS C 137 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied ALPHA1-2 " MAN D 4 " - " MAN D 5 " " MAN D 5 " - " MAN D 6 " ALPHA1-3 " BMA D 3 " - " MAN D 4 " " MAN D 6 " - " GLC D 7 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " NAG-ASN " NAG D 1 " - " ASN A 298 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.80 Conformation dependent library (CDL) restraints added in 213.0 milliseconds 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2000 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 10 sheets defined 43.4% alpha, 22.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 49 through 59 Processing helix chain 'A' and resid 61 through 81 removed outlier: 4.595A pdb=" N SER A 65 " --> pdb=" O GLU A 61 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE A 81 " --> pdb=" O CYS A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 104 removed outlier: 3.742A pdb=" N LEU A 102 " --> pdb=" O GLY A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 130 Processing helix chain 'A' and resid 149 through 154 Processing helix chain 'A' and resid 156 through 159 removed outlier: 3.903A pdb=" N ILE A 159 " --> pdb=" O SER A 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 156 through 159' Processing helix chain 'A' and resid 160 through 171 Processing helix chain 'A' and resid 172 through 175 removed outlier: 3.612A pdb=" N ASN A 175 " --> pdb=" O ALA A 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 172 through 175' Processing helix chain 'A' and resid 178 through 198 Processing helix chain 'A' and resid 223 through 237 removed outlier: 3.533A pdb=" N ILE A 227 " --> pdb=" O ASP A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 311 Processing helix chain 'B' and resid 4 through 9 removed outlier: 3.782A pdb=" N ASN B 8 " --> pdb=" O ALA B 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 35 removed outlier: 4.031A pdb=" N GLY B 32 " --> pdb=" O ALA B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 81 Processing helix chain 'B' and resid 121 through 125 removed outlier: 4.256A pdb=" N GLN B 125 " --> pdb=" O LEU B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 173 removed outlier: 3.591A pdb=" N GLU B 173 " --> pdb=" O PRO B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 258 removed outlier: 3.811A pdb=" N LYS B 232 " --> pdb=" O GLY B 228 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE B 240 " --> pdb=" O ALA B 236 " (cutoff:3.500A) Proline residue: B 243 - end of helix Processing helix chain 'B' and resid 264 through 282 Processing helix chain 'B' and resid 283 through 288 Processing helix chain 'B' and resid 295 through 321 removed outlier: 3.683A pdb=" N PHE B 307 " --> pdb=" O ARG B 303 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N SER B 313 " --> pdb=" O ALA B 309 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE B 316 " --> pdb=" O LEU B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 334 removed outlier: 3.599A pdb=" N GLY B 334 " --> pdb=" O HIS B 331 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 331 through 334' Processing helix chain 'B' and resid 335 through 358 Proline residue: B 341 - end of helix Processing helix chain 'B' and resid 359 through 362 Processing helix chain 'B' and resid 367 through 370 Processing helix chain 'B' and resid 371 through 412 Processing helix chain 'B' and resid 413 through 417 removed outlier: 3.769A pdb=" N MET B 417 " --> pdb=" O LEU B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 456 Processing helix chain 'B' and resid 469 through 492 Processing helix chain 'C' and resid 32 through 36 Processing helix chain 'C' and resid 196 through 200 Processing helix chain 'C' and resid 302 through 307 removed outlier: 3.722A pdb=" N ILE C 305 " --> pdb=" O ASP C 302 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TYR C 306 " --> pdb=" O PRO C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 377 removed outlier: 4.587A pdb=" N VAL C 349 " --> pdb=" O GLU C 345 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N THR C 350 " --> pdb=" O THR C 346 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ALA C 352 " --> pdb=" O GLY C 348 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ALA C 353 " --> pdb=" O VAL C 349 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS C 377 " --> pdb=" O ASP C 373 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 200 through 206 Processing sheet with id=AA2, first strand: chain 'A' and resid 254 through 258 removed outlier: 3.661A pdb=" N TYR A 273 " --> pdb=" O SER A 239 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 319 through 326 Processing sheet with id=AA4, first strand: chain 'B' and resid 40 through 46 removed outlier: 3.615A pdb=" N HIS B 225 " --> pdb=" O THR B 41 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU B 215 " --> pdb=" O ALA B 119 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ASP B 117 " --> pdb=" O LYS B 217 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N ILE B 219 " --> pdb=" O GLN B 115 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N GLN B 115 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N LEU B 221 " --> pdb=" O ILE B 113 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ILE B 113 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N GLY B 223 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU B 111 " --> pdb=" O GLY B 223 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N MET B 110 " --> pdb=" O GLU B 186 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLU B 186 " --> pdb=" O MET B 110 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N PHE B 112 " --> pdb=" O PHE B 184 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 73 through 74 removed outlier: 4.165A pdb=" N LYS B 49 " --> pdb=" O ILE B 74 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ARG B 200 " --> pdb=" O ASP B 135 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL B 132 " --> pdb=" O PRO B 157 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N MET B 134 " --> pdb=" O ARG B 155 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ARG B 155 " --> pdb=" O MET B 134 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N VAL B 136 " --> pdb=" O HIS B 153 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N HIS B 153 " --> pdb=" O VAL B 136 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N LEU B 138 " --> pdb=" O MET B 151 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 459 through 462 Processing sheet with id=AA7, first strand: chain 'C' and resid 21 through 25 Processing sheet with id=AA8, first strand: chain 'C' and resid 21 through 25 removed outlier: 4.272A pdb=" N PHE C 330 " --> pdb=" O GLN C 94 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N GLN C 94 " --> pdb=" O PHE C 330 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ILE C 332 " --> pdb=" O VAL C 92 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL C 92 " --> pdb=" O ILE C 332 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR C 181 " --> pdb=" O ARG C 177 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N TYR C 182 " --> pdb=" O SER C 193 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N SER C 193 " --> pdb=" O TYR C 182 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL C 184 " --> pdb=" O VAL C 191 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 37 through 39 removed outlier: 5.147A pdb=" N GLY C 312 " --> pdb=" O PHE C 81 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N TRP C 319 " --> pdb=" O GLY C 107 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 37 through 39 removed outlier: 5.147A pdb=" N GLY C 312 " --> pdb=" O PHE C 81 " (cutoff:3.500A) 459 hydrogen bonds defined for protein. 1275 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.25 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1414 1.31 - 1.43: 2568 1.43 - 1.56: 4962 1.56 - 1.69: 6 1.69 - 1.81: 105 Bond restraints: 9055 Sorted by residual: bond pdb=" C21 POV B 601 " pdb=" O21 POV B 601 " ideal model delta sigma weight residual 1.330 1.419 -0.089 2.00e-02 2.50e+03 2.00e+01 bond pdb=" C31 POV B 601 " pdb=" O31 POV B 601 " ideal model delta sigma weight residual 1.327 1.415 -0.088 2.00e-02 2.50e+03 1.93e+01 bond pdb="C210 POV B 601 " pdb="C211 POV B 601 " ideal model delta sigma weight residual 1.497 1.557 -0.060 2.00e-02 2.50e+03 9.10e+00 bond pdb=" C4 BMA D 3 " pdb=" C5 BMA D 3 " ideal model delta sigma weight residual 1.528 1.586 -0.058 2.00e-02 2.50e+03 8.47e+00 bond pdb=" N POV B 601 " pdb=" C14 POV B 601 " ideal model delta sigma weight residual 1.490 1.433 0.057 2.00e-02 2.50e+03 8.13e+00 ... (remaining 9050 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.66: 12000 2.66 - 5.33: 195 5.33 - 7.99: 23 7.99 - 10.65: 7 10.65 - 13.31: 3 Bond angle restraints: 12228 Sorted by residual: angle pdb=" CA PRO B 82 " pdb=" N PRO B 82 " pdb=" CD PRO B 82 " ideal model delta sigma weight residual 112.00 105.50 6.50 1.40e+00 5.10e-01 2.16e+01 angle pdb=" N PHE A 331 " pdb=" CA PHE A 331 " pdb=" C PHE A 331 " ideal model delta sigma weight residual 110.91 115.92 -5.01 1.17e+00 7.31e-01 1.83e+01 angle pdb=" CG ARG B 141 " pdb=" CD ARG B 141 " pdb=" NE ARG B 141 " ideal model delta sigma weight residual 112.00 120.80 -8.80 2.20e+00 2.07e-01 1.60e+01 angle pdb=" O13 POV B 601 " pdb=" P POV B 601 " pdb=" O14 POV B 601 " ideal model delta sigma weight residual 121.11 109.51 11.60 3.00e+00 1.11e-01 1.50e+01 angle pdb=" CA LEU C 367 " pdb=" CB LEU C 367 " pdb=" CG LEU C 367 " ideal model delta sigma weight residual 116.30 129.61 -13.31 3.50e+00 8.16e-02 1.45e+01 ... (remaining 12223 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 4751 17.82 - 35.65: 435 35.65 - 53.47: 104 53.47 - 71.29: 27 71.29 - 89.11: 10 Dihedral angle restraints: 5327 sinusoidal: 2218 harmonic: 3109 Sorted by residual: dihedral pdb=" CB CYS A 327 " pdb=" SG CYS A 327 " pdb=" SG CYS A 342 " pdb=" CB CYS A 342 " ideal model delta sinusoidal sigma weight residual 93.00 152.31 -59.31 1 1.00e+01 1.00e-02 4.70e+01 dihedral pdb=" CB CYS A 128 " pdb=" SG CYS A 128 " pdb=" SG CYS A 136 " pdb=" CB CYS A 136 " ideal model delta sinusoidal sigma weight residual -86.00 -144.59 58.59 1 1.00e+01 1.00e-02 4.60e+01 dihedral pdb=" CB CYS A 297 " pdb=" SG CYS A 297 " pdb=" SG CYS A 307 " pdb=" CB CYS A 307 " ideal model delta sinusoidal sigma weight residual 93.00 146.62 -53.62 1 1.00e+01 1.00e-02 3.91e+01 ... (remaining 5324 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 924 0.044 - 0.087: 282 0.087 - 0.131: 82 0.131 - 0.175: 9 0.175 - 0.219: 5 Chirality restraints: 1302 Sorted by residual: chirality pdb=" CA PRO B 82 " pdb=" N PRO B 82 " pdb=" C PRO B 82 " pdb=" CB PRO B 82 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.48 0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" C2 NAG D 1 " pdb=" C1 NAG D 1 " pdb=" C3 NAG D 1 " pdb=" N2 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.29 -0.20 2.00e-01 2.50e+01 9.74e-01 ... (remaining 1299 not shown) Planarity restraints: 1551 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 81 " 0.062 5.00e-02 4.00e+02 9.10e-02 1.32e+01 pdb=" N PRO B 82 " -0.157 5.00e-02 4.00e+02 pdb=" CA PRO B 82 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO B 82 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 36 " -0.042 5.00e-02 4.00e+02 6.50e-02 6.75e+00 pdb=" N PRO B 37 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO B 37 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 37 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 252 " 0.008 2.00e-02 2.50e+03 1.46e-02 5.30e+00 pdb=" CG TRP A 252 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP A 252 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP A 252 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 252 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 252 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 252 " 0.013 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 252 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 252 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 252 " -0.001 2.00e-02 2.50e+03 ... (remaining 1548 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1537 2.76 - 3.30: 8693 3.30 - 3.83: 14697 3.83 - 4.37: 16452 4.37 - 4.90: 29010 Nonbonded interactions: 70389 Sorted by model distance: nonbonded pdb=" NE1 TRP C 319 " pdb=" O4 BMA D 3 " model vdw 2.229 3.120 nonbonded pdb=" N SER B 133 " pdb=" OD1 ASN B 210 " model vdw 2.283 3.120 nonbonded pdb=" NE2 HIS A 332 " pdb=" OE2 GLU B 205 " model vdw 2.298 3.120 nonbonded pdb=" NZ LYS B 49 " pdb=" OD1 ASP B 218 " model vdw 2.326 3.120 nonbonded pdb=" O GLN C 70 " pdb=" OH TYR C 75 " model vdw 2.329 3.040 ... (remaining 70384 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.080 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 9078 Z= 0.254 Angle : 0.843 13.314 12279 Z= 0.426 Chirality : 0.047 0.219 1302 Planarity : 0.005 0.091 1550 Dihedral : 15.189 89.113 3282 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 0.53 % Allowed : 13.13 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.25), residues: 1071 helix: 1.16 (0.25), residues: 392 sheet: -0.55 (0.36), residues: 205 loop : -0.96 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 431 TYR 0.018 0.002 TYR B 140 PHE 0.026 0.002 PHE C 148 TRP 0.037 0.002 TRP A 252 HIS 0.006 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00561 / 0.25 ( 9055) covalent geometry : angle 0.83565 / 0.42 (12228) SS BOND : bond 0.00306 / 0.20 ( 15) SS BOND : angle 0.93532 / 0.54 ( 30) hydrogen bonds : bond 0.15344 / 10.14 ( 436) hydrogen bonds : angle 7.28379 / 5.21 ( 1275) Misc. bond : bond 0.00166 / 0.09 ( 1) link_ALPHA1-2 : bond 0.00521 / 0.27 ( 2) link_ALPHA1-2 : angle 1.65276 / 0.87 ( 6) link_ALPHA1-3 : bond 0.00083 / 0.04 ( 2) link_ALPHA1-3 : angle 2.22397 / 1.16 ( 6) link_BETA1-4 : bond 0.01150 / 0.58 ( 2) link_BETA1-4 : angle 2.63475 / 1.36 ( 6) link_NAG-ASN : bond 0.00064 / 0.03 ( 1) link_NAG-ASN : angle 4.66901 / 1.79 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 113 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 268 GLU cc_start: 0.6988 (mm-30) cc_final: 0.6093 (pp20) REVERT: B 128 GLU cc_start: 0.8702 (mm-30) cc_final: 0.8496 (mm-30) outliers start: 5 outliers final: 2 residues processed: 115 average time/residue: 0.0889 time to fit residues: 14.4254 Evaluate side-chains 107 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 105 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 438 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 30.0000 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 8.9990 chunk 106 optimal weight: 8.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 HIS C 99 HIS C 329 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.198058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.116335 restraints weight = 11838.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.114281 restraints weight = 6463.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.115393 restraints weight = 4764.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.116762 restraints weight = 3999.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.116716 restraints weight = 3440.892| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.1002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9078 Z= 0.140 Angle : 0.649 10.419 12279 Z= 0.327 Chirality : 0.044 0.268 1302 Planarity : 0.004 0.043 1550 Dihedral : 7.759 86.327 1212 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.81 % Allowed : 13.55 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.25), residues: 1071 helix: 1.32 (0.25), residues: 406 sheet: -0.44 (0.37), residues: 184 loop : -1.08 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 141 TYR 0.012 0.001 TYR C 150 PHE 0.020 0.001 PHE C 113 TRP 0.024 0.002 TRP C 200 HIS 0.004 0.001 HIS A 332 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 ( 9055) covalent geometry : angle 0.64309 / 0.33 (12228) SS BOND : bond 0.00240 / 0.17 ( 15) SS BOND : angle 0.87796 / 0.49 ( 30) hydrogen bonds : bond 0.04285 / 2.94 ( 436) hydrogen bonds : angle 5.24782 / 3.78 ( 1275) Misc. bond : bond 0.00107 / 0.06 ( 1) link_ALPHA1-2 : bond 0.01006 / 0.52 ( 2) link_ALPHA1-2 : angle 1.36791 / 0.72 ( 6) link_ALPHA1-3 : bond 0.00092 / 0.04 ( 2) link_ALPHA1-3 : angle 1.89987 / 1.03 ( 6) link_BETA1-4 : bond 0.00936 / 0.47 ( 2) link_BETA1-4 : angle 1.96744 / 1.04 ( 6) link_NAG-ASN : bond 0.00151 / 0.08 ( 1) link_NAG-ASN : angle 3.45238 / 1.33 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 0.213 Fit side-chains REVERT: A 42 CYS cc_start: 0.5102 (OUTLIER) cc_final: 0.4888 (m) REVERT: A 324 ARG cc_start: 0.7854 (ttp80) cc_final: 0.7653 (ttp80) REVERT: B 128 GLU cc_start: 0.8745 (mm-30) cc_final: 0.8528 (mm-30) REVERT: B 379 MET cc_start: 0.8167 (tpp) cc_final: 0.7919 (tpt) outliers start: 17 outliers final: 9 residues processed: 122 average time/residue: 0.0690 time to fit residues: 12.2536 Evaluate side-chains 109 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 185 MET Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 146 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 51 optimal weight: 0.2980 chunk 32 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 83 optimal weight: 30.0000 chunk 73 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 39 optimal weight: 0.3980 chunk 55 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 96 optimal weight: 30.0000 chunk 79 optimal weight: 0.6980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 ASN C 99 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.197600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.115510 restraints weight = 11987.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.113263 restraints weight = 6536.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.115110 restraints weight = 4873.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.116018 restraints weight = 3872.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.116101 restraints weight = 3492.514| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9078 Z= 0.144 Angle : 0.619 12.629 12279 Z= 0.311 Chirality : 0.043 0.279 1302 Planarity : 0.004 0.041 1550 Dihedral : 7.234 81.134 1209 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.03 % Allowed : 14.73 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.25), residues: 1071 helix: 1.44 (0.25), residues: 406 sheet: -0.59 (0.35), residues: 207 loop : -1.07 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 141 TYR 0.011 0.001 TYR B 484 PHE 0.022 0.001 PHE C 46 TRP 0.024 0.001 TRP C 200 HIS 0.006 0.001 HIS C 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 ( 9055) covalent geometry : angle 0.61376 / 0.31 (12228) SS BOND : bond 0.00255 / 0.15 ( 15) SS BOND : angle 0.77010 / 0.44 ( 30) hydrogen bonds : bond 0.03948 / 2.68 ( 436) hydrogen bonds : angle 4.94475 / 3.55 ( 1275) Misc. bond : bond 0.00075 / 0.04 ( 1) link_ALPHA1-2 : bond 0.00720 / 0.37 ( 2) link_ALPHA1-2 : angle 1.41821 / 0.76 ( 6) link_ALPHA1-3 : bond 0.00146 / 0.08 ( 2) link_ALPHA1-3 : angle 1.80952 / 0.97 ( 6) link_BETA1-4 : bond 0.00935 / 0.48 ( 2) link_BETA1-4 : angle 1.88805 / 1.00 ( 6) link_NAG-ASN : bond 0.00158 / 0.08 ( 1) link_NAG-ASN : angle 2.79759 / 1.04 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 0.310 Fit side-chains REVERT: B 140 TYR cc_start: 0.8368 (p90) cc_final: 0.8085 (p90) REVERT: B 154 GLU cc_start: 0.7110 (mt-10) cc_final: 0.6830 (mt-10) REVERT: B 379 MET cc_start: 0.8155 (tpp) cc_final: 0.7936 (tpt) outliers start: 19 outliers final: 13 residues processed: 125 average time/residue: 0.0724 time to fit residues: 13.2960 Evaluate side-chains 116 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 185 MET Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 319 CYS Chi-restraints excluded: chain C residue 122 MET Chi-restraints excluded: chain C residue 146 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 71 optimal weight: 2.9990 chunk 13 optimal weight: 9.9990 chunk 89 optimal weight: 8.9990 chunk 28 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 45 optimal weight: 0.0060 chunk 66 optimal weight: 0.9980 chunk 36 optimal weight: 10.0000 chunk 81 optimal weight: 8.9990 chunk 53 optimal weight: 0.9990 chunk 85 optimal weight: 20.0000 overall best weight: 1.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 184 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.195877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.112609 restraints weight = 12024.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.112939 restraints weight = 5909.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.114167 restraints weight = 4309.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.114256 restraints weight = 3666.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.114393 restraints weight = 3629.907| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9078 Z= 0.176 Angle : 0.628 13.881 12279 Z= 0.314 Chirality : 0.044 0.283 1302 Planarity : 0.004 0.038 1550 Dihedral : 6.945 78.637 1209 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.52 % Allowed : 14.30 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.25), residues: 1071 helix: 1.41 (0.25), residues: 409 sheet: -0.58 (0.36), residues: 204 loop : -1.07 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 141 TYR 0.013 0.001 TYR B 484 PHE 0.018 0.001 PHE C 113 TRP 0.028 0.002 TRP C 200 HIS 0.005 0.001 HIS A 332 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.18 ( 9055) covalent geometry : angle 0.62362 / 0.31 (12228) SS BOND : bond 0.00439 / 0.21 ( 15) SS BOND : angle 0.80336 / 0.45 ( 30) hydrogen bonds : bond 0.03832 / 2.59 ( 436) hydrogen bonds : angle 4.85045 / 3.49 ( 1275) Misc. bond : bond 0.00106 / 0.06 ( 1) link_ALPHA1-2 : bond 0.00696 / 0.35 ( 2) link_ALPHA1-2 : angle 1.38580 / 0.73 ( 6) link_ALPHA1-3 : bond 0.00159 / 0.08 ( 2) link_ALPHA1-3 : angle 1.77308 / 0.94 ( 6) link_BETA1-4 : bond 0.01063 / 0.54 ( 2) link_BETA1-4 : angle 1.75700 / 0.94 ( 6) link_NAG-ASN : bond 0.00118 / 0.06 ( 1) link_NAG-ASN : angle 2.56149 / 0.91 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 108 time to evaluate : 0.227 Fit side-chains REVERT: A 184 ASN cc_start: 0.8746 (m110) cc_final: 0.8475 (m110) REVERT: A 241 MET cc_start: 0.7886 (OUTLIER) cc_final: 0.7091 (ppp) REVERT: B 140 TYR cc_start: 0.8468 (p90) cc_final: 0.8049 (p90) REVERT: B 154 GLU cc_start: 0.7180 (mt-10) cc_final: 0.6977 (mt-10) REVERT: B 161 LYS cc_start: 0.7365 (tptp) cc_final: 0.7134 (tptt) REVERT: B 205 GLU cc_start: 0.7916 (mp0) cc_final: 0.7625 (mp0) REVERT: B 445 MET cc_start: 0.6297 (ttm) cc_final: 0.6047 (ttp) outliers start: 33 outliers final: 23 residues processed: 128 average time/residue: 0.0702 time to fit residues: 13.3396 Evaluate side-chains 128 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 104 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 185 MET Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 319 CYS Chi-restraints excluded: chain B residue 383 ILE Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain C residue 122 MET Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 318 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 95 optimal weight: 40.0000 chunk 96 optimal weight: 20.0000 chunk 44 optimal weight: 1.9990 chunk 83 optimal weight: 0.0770 chunk 16 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 chunk 72 optimal weight: 0.0170 chunk 47 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.198208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.116973 restraints weight = 12051.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.114706 restraints weight = 6443.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.115962 restraints weight = 4607.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.116983 restraints weight = 4001.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.116982 restraints weight = 3493.363| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9078 Z= 0.122 Angle : 0.593 14.429 12279 Z= 0.292 Chirality : 0.042 0.280 1302 Planarity : 0.004 0.034 1550 Dihedral : 6.550 72.125 1209 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.77 % Allowed : 16.12 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.25), residues: 1071 helix: 1.63 (0.25), residues: 410 sheet: -0.45 (0.36), residues: 204 loop : -1.10 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 141 TYR 0.009 0.001 TYR B 492 PHE 0.017 0.001 PHE C 113 TRP 0.025 0.002 TRP C 200 HIS 0.004 0.001 HIS A 332 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 9055) covalent geometry : angle 0.58903 / 0.29 (12228) SS BOND : bond 0.00232 / 0.14 ( 15) SS BOND : angle 0.73995 / 0.43 ( 30) hydrogen bonds : bond 0.03505 / 2.36 ( 436) hydrogen bonds : angle 4.65759 / 3.34 ( 1275) Misc. bond : bond 0.00053 / 0.03 ( 1) link_ALPHA1-2 : bond 0.00648 / 0.33 ( 2) link_ALPHA1-2 : angle 1.40880 / 0.76 ( 6) link_ALPHA1-3 : bond 0.00195 / 0.10 ( 2) link_ALPHA1-3 : angle 1.68982 / 0.89 ( 6) link_BETA1-4 : bond 0.00905 / 0.46 ( 2) link_BETA1-4 : angle 1.64701 / 0.87 ( 6) link_NAG-ASN : bond 0.00194 / 0.10 ( 1) link_NAG-ASN : angle 2.16772 / 0.77 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 110 time to evaluate : 0.414 Fit side-chains REVERT: A 331 PHE cc_start: 0.8428 (OUTLIER) cc_final: 0.8137 (m-10) REVERT: B 128 GLU cc_start: 0.8759 (mm-30) cc_final: 0.8549 (mm-30) REVERT: B 140 TYR cc_start: 0.8374 (p90) cc_final: 0.7979 (p90) REVERT: B 205 GLU cc_start: 0.7909 (mp0) cc_final: 0.7704 (mp0) REVERT: B 489 MET cc_start: 0.6957 (mtt) cc_final: 0.6647 (mtt) REVERT: C 77 LEU cc_start: 0.3196 (OUTLIER) cc_final: 0.2814 (mm) outliers start: 26 outliers final: 18 residues processed: 126 average time/residue: 0.0599 time to fit residues: 11.2676 Evaluate side-chains 124 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 185 MET Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 319 CYS Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain C residue 56 PHE Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 122 MET Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 318 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 99 optimal weight: 7.9990 chunk 30 optimal weight: 7.9990 chunk 95 optimal weight: 10.0000 chunk 7 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 58 optimal weight: 0.5980 chunk 45 optimal weight: 0.3980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.198602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.116875 restraints weight = 12003.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.114396 restraints weight = 6986.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.117988 restraints weight = 4860.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.117543 restraints weight = 3513.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.117893 restraints weight = 3315.663| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9078 Z= 0.121 Angle : 0.586 12.614 12279 Z= 0.289 Chirality : 0.042 0.280 1302 Planarity : 0.004 0.034 1550 Dihedral : 6.286 65.955 1209 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.52 % Allowed : 16.01 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.25), residues: 1071 helix: 1.72 (0.25), residues: 410 sheet: -0.41 (0.36), residues: 206 loop : -1.09 (0.27), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 141 TYR 0.010 0.001 TYR C 109 PHE 0.022 0.001 PHE C 148 TRP 0.025 0.002 TRP C 200 HIS 0.004 0.001 HIS C 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 ( 9055) covalent geometry : angle 0.58222 / 0.29 (12228) SS BOND : bond 0.00207 / 0.13 ( 15) SS BOND : angle 0.75542 / 0.44 ( 30) hydrogen bonds : bond 0.03387 / 2.28 ( 436) hydrogen bonds : angle 4.57948 / 3.28 ( 1275) Misc. bond : bond 0.00072 / 0.04 ( 1) link_ALPHA1-2 : bond 0.00569 / 0.29 ( 2) link_ALPHA1-2 : angle 1.42390 / 0.76 ( 6) link_ALPHA1-3 : bond 0.00212 / 0.11 ( 2) link_ALPHA1-3 : angle 1.66058 / 0.89 ( 6) link_BETA1-4 : bond 0.00872 / 0.44 ( 2) link_BETA1-4 : angle 1.53560 / 0.81 ( 6) link_NAG-ASN : bond 0.00212 / 0.11 ( 1) link_NAG-ASN : angle 1.95388 / 0.68 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 111 time to evaluate : 0.275 Fit side-chains REVERT: A 241 MET cc_start: 0.7296 (OUTLIER) cc_final: 0.6671 (ptm) REVERT: A 331 PHE cc_start: 0.8421 (OUTLIER) cc_final: 0.8187 (m-10) REVERT: B 140 TYR cc_start: 0.8435 (p90) cc_final: 0.7972 (p90) REVERT: B 141 ARG cc_start: 0.7766 (ttp-170) cc_final: 0.7243 (ttp-170) REVERT: B 154 GLU cc_start: 0.7254 (mt-10) cc_final: 0.6477 (mt-10) REVERT: C 77 LEU cc_start: 0.3324 (OUTLIER) cc_final: 0.2954 (mm) outliers start: 33 outliers final: 22 residues processed: 133 average time/residue: 0.0675 time to fit residues: 13.3490 Evaluate side-chains 129 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 104 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 185 MET Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 319 CYS Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain C residue 56 PHE Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 122 MET Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 318 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 78 optimal weight: 1.9990 chunk 64 optimal weight: 0.1980 chunk 0 optimal weight: 20.0000 chunk 60 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 104 optimal weight: 8.9990 chunk 37 optimal weight: 3.9990 chunk 88 optimal weight: 20.0000 chunk 65 optimal weight: 0.9990 chunk 36 optimal weight: 10.0000 chunk 93 optimal weight: 0.0270 overall best weight: 0.8242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 340 GLN ** B 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.198831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.117061 restraints weight = 12123.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.114771 restraints weight = 6950.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.118105 restraints weight = 4882.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.117883 restraints weight = 3517.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.118139 restraints weight = 3345.407| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9078 Z= 0.121 Angle : 0.593 15.888 12279 Z= 0.289 Chirality : 0.042 0.280 1302 Planarity : 0.003 0.034 1550 Dihedral : 6.047 56.889 1209 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 3.31 % Allowed : 16.86 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.26), residues: 1071 helix: 1.81 (0.25), residues: 409 sheet: -0.40 (0.36), residues: 209 loop : -1.12 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 141 TYR 0.013 0.001 TYR B 492 PHE 0.031 0.001 PHE B 318 TRP 0.026 0.002 TRP C 200 HIS 0.004 0.001 HIS C 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 ( 9055) covalent geometry : angle 0.58992 / 0.29 (12228) SS BOND : bond 0.00218 / 0.14 ( 15) SS BOND : angle 0.71313 / 0.42 ( 30) hydrogen bonds : bond 0.03321 / 2.23 ( 436) hydrogen bonds : angle 4.48901 / 3.21 ( 1275) Misc. bond : bond 0.00075 / 0.04 ( 1) link_ALPHA1-2 : bond 0.00525 / 0.27 ( 2) link_ALPHA1-2 : angle 1.50277 / 0.80 ( 6) link_ALPHA1-3 : bond 0.00215 / 0.11 ( 2) link_ALPHA1-3 : angle 1.52822 / 0.80 ( 6) link_BETA1-4 : bond 0.00840 / 0.43 ( 2) link_BETA1-4 : angle 1.47411 / 0.78 ( 6) link_NAG-ASN : bond 0.00238 / 0.13 ( 1) link_NAG-ASN : angle 1.75073 / 0.59 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 109 time to evaluate : 0.220 Fit side-chains revert: symmetry clash REVERT: A 302 HIS cc_start: 0.5479 (t70) cc_final: 0.5233 (t70) REVERT: A 331 PHE cc_start: 0.8403 (OUTLIER) cc_final: 0.8163 (m-10) REVERT: B 46 MET cc_start: 0.8159 (tpp) cc_final: 0.7926 (tpp) REVERT: B 140 TYR cc_start: 0.8441 (p90) cc_final: 0.7923 (p90) REVERT: B 141 ARG cc_start: 0.7800 (ttp-170) cc_final: 0.7229 (ttp-170) REVERT: B 154 GLU cc_start: 0.7128 (mt-10) cc_final: 0.6407 (mt-10) REVERT: C 77 LEU cc_start: 0.3375 (OUTLIER) cc_final: 0.2979 (mm) outliers start: 31 outliers final: 19 residues processed: 131 average time/residue: 0.0722 time to fit residues: 13.7518 Evaluate side-chains 126 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 105 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 185 MET Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 319 CYS Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain C residue 56 PHE Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 122 MET Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 318 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 31 optimal weight: 0.0970 chunk 18 optimal weight: 0.0470 chunk 53 optimal weight: 0.7980 chunk 88 optimal weight: 8.9990 chunk 33 optimal weight: 2.9990 chunk 58 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 21 optimal weight: 7.9990 chunk 3 optimal weight: 0.9980 chunk 99 optimal weight: 9.9990 chunk 4 optimal weight: 1.9990 overall best weight: 0.5076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 424 HIS ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.199808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.114077 restraints weight = 11607.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.118900 restraints weight = 5127.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.122012 restraints weight = 3324.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.123698 restraints weight = 2637.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.124485 restraints weight = 2343.930| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9078 Z= 0.106 Angle : 0.572 14.848 12279 Z= 0.278 Chirality : 0.042 0.278 1302 Planarity : 0.003 0.036 1550 Dihedral : 5.681 47.323 1209 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.77 % Allowed : 17.08 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.26), residues: 1071 helix: 2.24 (0.25), residues: 395 sheet: -0.24 (0.37), residues: 208 loop : -0.96 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 261 TYR 0.015 0.001 TYR A 346 PHE 0.029 0.001 PHE B 318 TRP 0.028 0.002 TRP B 336 HIS 0.004 0.001 HIS C 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 ( 9055) covalent geometry : angle 0.56892 / 0.28 (12228) SS BOND : bond 0.00205 / 0.14 ( 15) SS BOND : angle 0.70255 / 0.42 ( 30) hydrogen bonds : bond 0.03142 / 2.11 ( 436) hydrogen bonds : angle 4.33987 / 3.10 ( 1275) Misc. bond : bond 0.00062 / 0.03 ( 1) link_ALPHA1-2 : bond 0.00513 / 0.26 ( 2) link_ALPHA1-2 : angle 1.51708 / 0.82 ( 6) link_ALPHA1-3 : bond 0.00292 / 0.15 ( 2) link_ALPHA1-3 : angle 1.46643 / 0.77 ( 6) link_BETA1-4 : bond 0.00838 / 0.42 ( 2) link_BETA1-4 : angle 1.45032 / 0.76 ( 6) link_NAG-ASN : bond 0.00290 / 0.15 ( 1) link_NAG-ASN : angle 1.48692 / 0.50 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 111 time to evaluate : 0.355 Fit side-chains REVERT: A 184 ASN cc_start: 0.8573 (m110) cc_final: 0.8332 (m110) REVERT: A 331 PHE cc_start: 0.8316 (OUTLIER) cc_final: 0.7936 (m-10) REVERT: B 66 TRP cc_start: 0.8104 (p-90) cc_final: 0.7826 (p90) REVERT: B 140 TYR cc_start: 0.8411 (p90) cc_final: 0.7862 (p90) REVERT: B 141 ARG cc_start: 0.7755 (ttp-170) cc_final: 0.7165 (ttp-170) REVERT: B 154 GLU cc_start: 0.7031 (mt-10) cc_final: 0.6354 (mt-10) REVERT: B 489 MET cc_start: 0.7040 (mtt) cc_final: 0.6687 (mtt) REVERT: C 77 LEU cc_start: 0.3342 (OUTLIER) cc_final: 0.2925 (mm) outliers start: 26 outliers final: 19 residues processed: 128 average time/residue: 0.0739 time to fit residues: 13.7347 Evaluate side-chains 123 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 102 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 185 MET Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 319 CYS Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 56 PHE Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 122 MET Chi-restraints excluded: chain C residue 318 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 50 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 chunk 26 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 83 optimal weight: 20.0000 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.197704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.117287 restraints weight = 11608.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.116077 restraints weight = 6290.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.116462 restraints weight = 4872.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.117691 restraints weight = 4143.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.117788 restraints weight = 3576.132| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9078 Z= 0.140 Angle : 0.606 14.687 12279 Z= 0.296 Chirality : 0.042 0.265 1302 Planarity : 0.004 0.035 1550 Dihedral : 5.746 47.566 1209 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.52 % Allowed : 17.50 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.26), residues: 1071 helix: 2.13 (0.25), residues: 395 sheet: -0.15 (0.37), residues: 206 loop : -0.97 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 257 TYR 0.010 0.001 TYR B 478 PHE 0.033 0.001 PHE B 318 TRP 0.029 0.002 TRP B 336 HIS 0.006 0.001 HIS A 302 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 ( 9055) covalent geometry : angle 0.60357 / 0.30 (12228) SS BOND : bond 0.00229 / 0.15 ( 15) SS BOND : angle 0.70466 / 0.41 ( 30) hydrogen bonds : bond 0.03348 / 2.24 ( 436) hydrogen bonds : angle 4.40065 / 3.14 ( 1275) Misc. bond : bond 0.00089 / 0.05 ( 1) link_ALPHA1-2 : bond 0.00467 / 0.23 ( 2) link_ALPHA1-2 : angle 1.51946 / 0.80 ( 6) link_ALPHA1-3 : bond 0.00216 / 0.11 ( 2) link_ALPHA1-3 : angle 1.45102 / 0.76 ( 6) link_BETA1-4 : bond 0.00663 / 0.33 ( 2) link_BETA1-4 : angle 1.26093 / 0.66 ( 6) link_NAG-ASN : bond 0.00462 / 0.24 ( 1) link_NAG-ASN : angle 1.66341 / 0.61 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 105 time to evaluate : 0.237 Fit side-chains REVERT: A 331 PHE cc_start: 0.8213 (OUTLIER) cc_final: 0.7988 (m-10) REVERT: B 140 TYR cc_start: 0.8447 (p90) cc_final: 0.7828 (p90) REVERT: B 141 ARG cc_start: 0.7791 (ttp-170) cc_final: 0.7212 (ttp-170) REVERT: B 154 GLU cc_start: 0.7092 (mt-10) cc_final: 0.6410 (mt-10) REVERT: B 426 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7894 (tm-30) REVERT: B 445 MET cc_start: 0.6391 (ttm) cc_final: 0.6171 (ttp) REVERT: C 77 LEU cc_start: 0.3175 (OUTLIER) cc_final: 0.2726 (mm) outliers start: 33 outliers final: 24 residues processed: 127 average time/residue: 0.0697 time to fit residues: 12.9145 Evaluate side-chains 129 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 102 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 185 MET Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 319 CYS Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 426 GLU Chi-restraints excluded: chain C residue 56 PHE Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 122 MET Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 318 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 84 optimal weight: 40.0000 chunk 58 optimal weight: 0.8980 chunk 47 optimal weight: 0.4980 chunk 33 optimal weight: 2.9990 chunk 81 optimal weight: 10.0000 chunk 82 optimal weight: 20.0000 chunk 3 optimal weight: 0.6980 chunk 76 optimal weight: 3.9990 chunk 61 optimal weight: 0.5980 chunk 92 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.199133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.113234 restraints weight = 11605.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.117979 restraints weight = 5150.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.121026 restraints weight = 3352.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.122781 restraints weight = 2665.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.123636 restraints weight = 2363.419| |-----------------------------------------------------------------------------| r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9078 Z= 0.118 Angle : 0.602 14.542 12279 Z= 0.291 Chirality : 0.042 0.272 1302 Planarity : 0.003 0.037 1550 Dihedral : 5.662 46.264 1209 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.99 % Allowed : 18.25 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.26), residues: 1071 helix: 2.36 (0.25), residues: 388 sheet: -0.14 (0.37), residues: 204 loop : -0.90 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 177 TYR 0.009 0.001 TYR B 492 PHE 0.031 0.001 PHE B 318 TRP 0.029 0.002 TRP B 336 HIS 0.005 0.001 HIS C 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 ( 9055) covalent geometry : angle 0.59912 / 0.29 (12228) SS BOND : bond 0.00204 / 0.14 ( 15) SS BOND : angle 0.69530 / 0.41 ( 30) hydrogen bonds : bond 0.03274 / 2.20 ( 436) hydrogen bonds : angle 4.34219 / 3.10 ( 1275) Misc. bond : bond 0.00072 / 0.04 ( 1) link_ALPHA1-2 : bond 0.00474 / 0.24 ( 2) link_ALPHA1-2 : angle 1.51405 / 0.81 ( 6) link_ALPHA1-3 : bond 0.00270 / 0.14 ( 2) link_ALPHA1-3 : angle 1.43055 / 0.75 ( 6) link_BETA1-4 : bond 0.00754 / 0.38 ( 2) link_BETA1-4 : angle 1.35157 / 0.69 ( 6) link_NAG-ASN : bond 0.00384 / 0.20 ( 1) link_NAG-ASN : angle 1.61875 / 0.57 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 105 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 140 TYR cc_start: 0.8419 (p90) cc_final: 0.7825 (p90) REVERT: B 154 GLU cc_start: 0.6993 (mt-10) cc_final: 0.6359 (mt-10) REVERT: B 426 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7885 (tm-30) REVERT: C 77 LEU cc_start: 0.3371 (OUTLIER) cc_final: 0.2964 (mm) outliers start: 28 outliers final: 23 residues processed: 123 average time/residue: 0.0687 time to fit residues: 12.3623 Evaluate side-chains 129 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 104 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 185 MET Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 319 CYS Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 426 GLU Chi-restraints excluded: chain C residue 56 PHE Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 122 MET Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 318 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 41 optimal weight: 0.0770 chunk 12 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 chunk 104 optimal weight: 8.9990 chunk 84 optimal weight: 30.0000 chunk 49 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 50 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 5 optimal weight: 9.9990 chunk 65 optimal weight: 0.6980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 184 ASN C 99 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.200351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.112776 restraints weight = 11831.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.117621 restraints weight = 5353.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.120760 restraints weight = 3532.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.122523 restraints weight = 2835.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.123132 restraints weight = 2534.844| |-----------------------------------------------------------------------------| r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9078 Z= 0.114 Angle : 0.599 14.293 12279 Z= 0.290 Chirality : 0.042 0.279 1302 Planarity : 0.003 0.037 1550 Dihedral : 5.505 44.787 1209 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.99 % Allowed : 18.14 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.26), residues: 1071 helix: 2.40 (0.25), residues: 388 sheet: 0.03 (0.38), residues: 200 loop : -0.90 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 177 TYR 0.010 0.001 TYR B 492 PHE 0.031 0.001 PHE B 318 TRP 0.028 0.002 TRP B 336 HIS 0.005 0.001 HIS C 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 ( 9055) covalent geometry : angle 0.59600 / 0.29 (12228) SS BOND : bond 0.00194 / 0.13 ( 15) SS BOND : angle 0.69032 / 0.41 ( 30) hydrogen bonds : bond 0.03185 / 2.13 ( 436) hydrogen bonds : angle 4.28971 / 3.06 ( 1275) Misc. bond : bond 0.00067 / 0.04 ( 1) link_ALPHA1-2 : bond 0.00471 / 0.24 ( 2) link_ALPHA1-2 : angle 1.53410 / 0.82 ( 6) link_ALPHA1-3 : bond 0.00289 / 0.15 ( 2) link_ALPHA1-3 : angle 1.39221 / 0.73 ( 6) link_BETA1-4 : bond 0.00759 / 0.38 ( 2) link_BETA1-4 : angle 1.35073 / 0.69 ( 6) link_NAG-ASN : bond 0.00366 / 0.19 ( 1) link_NAG-ASN : angle 1.56340 / 0.55 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1595.23 seconds wall clock time: 28 minutes 6.94 seconds (1686.94 seconds total)